Some of them, like Tendi, I think have a solid basis for being intersex. Others are more just for fun. I as an ipsogender intersex person like to see intersex representation!
Let's start with DS9 because it's my favourite. 💛💜💛
Nog
At no point in DS9 is it ever explained why Nog is so much shorter than other Ferengi. And like Jean-Luc's bald head I think that is great. Normalise bodily variation. It doesn't need to be explained. People can just be.
Real life Aron Eisenberg (Nog's actor) said his growth was stunted due to a malfunctioning kidney. But in my headcanon, Nog is short due to some form of Ferengi hypogonadism. I'm thinking something like Kallman Syndrome. But Ferengi.
Julian Bashir
Trans Julian is a common headcanon. I dig it. And I say: "yes, and" to it! Intersex people can be trans too! (I have him with the ultergender flag here.)
We know young Julian had a developmental disability including learning difficulties. This is canon. Some intersex variations (usually the chromosomal variations) do have higher levels of LDs and/or slow development.
What jives for me is XXYY Syndrome - it's associated with being taller than usual, developmental delays, ADHD, and autism. Sounds to me like our dear doctor.
Elim Garak
Okay so his big titties are a meme in DS9 fandom. I have lost track of how many tumblr posts I have seen (and reblogged) about them. And Garak's build is shorter and stockier than the other Cardassian men we see.
I'm thinking he would have an intersex variation that shows up at puberty. De la Chapelle Syndrome in human men is associated with breast growth and a puberty that isn't quite like the usual testosterone puberty. So maybe a Cardassian version of that, or similar.
Phlox
Speaking of men with tiddies. Phlox comes from a very sex-positive society and I like to think it is totally nbd to be intersex there, to the point where it never crosses his mind that it could be an identity.
In my mind he's got a Denobulan equivalent of XXY (Klinefelter syndrome). XXY folks tend to have less body hair and be taller than average, and their intersex-ness tends to be less obvious (at least compared to XXYY, XYY, etc). We haven't seen that many Denobulans on-screen to gauge how his body hair compares to other Denobulan men but it seems totally plausible to me.
It also just makes me happy to envision intersex representation where the person's intersex traits are fairly subtle actually? That's pretty common for intersex people and I just wanna see more boring intersex bodies.
Jett Reno
So unless I've missed something, Reno's flat chest has not been explained in Discovery. Real life Tig Notaro had breast cancer. But this is the future! Surely breast cancer wouldn't be a thing. (Right???)
So to me that means either she had breasts and had them removed, or she never had them. Honestly in terms of probability, it's probably the former. But I like the idea she has Aromatase Deficiency, and just never developed breasts. Aromatase Deficiency is also highly correlated with osteoporosis and this also tracks with her various back/etc pains.
I've put her with the intergender flag because even with my intersex headcanon she still has strong nonbinary vibes for me. If she grew up sans breasts it's worth noting she chose to leave them that way.
D'Vana Tendi
Now here's a character where I think it's pretty clearly implied they are intersex. Tendi's on-screen reaction to whether she can use her female Orion pheromones was that "I’m not even that kind of Orion."
And when in a later episode she's asked about her female pheromones she says outright "We don't all have those!".
Rok-Tahk
Rok-Tahk's very introduction on ST:Prodigy is Dal mistaking her for an adult male. And sure, Dal hasn't talked to the Brikar much, but he has been around them his whole life.
So I interpret this as Rok has some sort of intersex variation that has sped up her physical growth - probably a form of hypergonadism.
So far we've only had one season of Prodigy and don't know that much about the Brikar yet so I'm not sure whether hypeestrogenism, hyperandrogenism, or Aromatase Exccess Syndrome would be the closest analogue to Brikar physiology. I think all of them seem plausible so far - again, given she is an alien and things would probably be a bit different than for humans.
Final Thoughts
My expectation is that whoever winds up being the first canonically intersex character in Trek, they're more likely to be a new character rather than a well-established one. Fingers crossed for Rok-Tahk and Tendi!
If I've missed any potentially intersex characters in Trek let me know! Fun headcanons too!